Compositions and methods for regulating gene expression for targeted mutagenesis

Abstract

Disclosed herein are methods for gene targeting in a plant cell, as well as recombinant nucleic acid molecules used in these methods. Further disclosed are recombinant nucleic acid molecules comprising a target gene operably linked to a regulatory region of the UBQ10 gene.

What is claimed is: 
     
       1. A method for gene targeting in a plant cell, the method comprising:
 (a) introducing into said plant cell a first nucleic acid comprising a viral replicon comprising a donor nucleic acid sequence, said donor sequence targeted to an endogenous DNA sequence in said plant cell; and 
 (b) introducing into said plant cell a second nucleic acid comprising a nuclease system, wherein said nuclease system is targeted to said endogenous DNA sequence, and wherein at least one component of said nuclease system is expressed under the control of a POLYUBIQUITIN10 (UBQ10) gene regulatory sequence; 
 
       wherein homologous recombination occurs between the donor sequence and said plant endogenous DNA sequence, 
       wherein said UBQ10 gene regulatory sequence comprises a recombinant nucleic acid molecule comprising:
 (i) a first regulatory region, wherein said first regulatory region comprises a first nucleic acid sequence from a UBQ10 gene wherein said first nucleic acid sequence extends about 2 Kb upstream of the coding region of said UBQ10 gene but not including the start codon, and wherein said first regulatory region is 5′ of said at least one component of said nuclease system; and 
 (ii) a second regulatory region, wherein said second regulatory region comprises a second nucleic acid sequence from said UBQ10 gene wherein said second nucleic acid sequence extends about 1 Kb downstream of the coding region of said UBQ10 gene but not including the stop codon of said UBQ10 gene, and wherein said second regulatory region is 3′ of said at least one component of said nuclease system; 
 
       wherein said UBQ10 gene comprises the sequence set forth in nucleic acids 2076-3449 of SEQ ID NO: 22 or a homolog thereof having at least 90% identity with nucleic acids 2076-3449 of SEQ ID NO: 22, 
       wherein said nuclease system is selected from a nickase, a CRISPR/Cas system, or a DNA endonuclease enzyme used in targeted gene editing, and 
       wherein said viral replicon is selected from the group consisting of: a geminiviral replicon, a bean yellow dwarf virus (BeYDV) replicon, a cabbage leaf curl virus (CalCuV) replicon, a tomato leaf curl virus (ToLCV) replicon, a wheat dwarf virus (WDV) replicon, or any combination thereof. 
     
     
       2. The method of  claim 1 , wherein said donor sequence comprises a gene, a mutated gene, a part of a gene, a regulatory sequence, a mutated regulatory sequence, a sequence upstream of a gene, a sequence downstream of a gene, an exon sequence, an intron sequence, or any combination thereof. 
     
     
       3. The method of  claim 1 , wherein said CRISPR/Cas system comprises a Cas nuclease and a gRNA molecule, wherein said gRNA molecule binds within said plant endogenous DNA sequence. 
     
     
       4. The method of  claim 3 , wherein said Cas nuclease is selected from the group consisting of Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9, Cas10, C2d, CasX, NgAgo, Cpf1, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csxl6, CsaX, Csx3, Csx1, Csxl5, Csf1, Csf2, Csf3, and Csf4. 
     
     
       5. The method of  claim 1 , wherein said at least one component of said nuclease system comprises a Cas nuclease. 
     
     
       6. The method of  claim 1 , wherein a single expression vector comprises said first nucleic acid and said second nucleic acid. 
     
     
       7. The method of  claim 1 , wherein said UBQ10 gene regulatory sequence comprises a  Solanum lycopersicum  or a  Solamum luberosum  UBQ10 gene regulatory sequence. 
     
     
       8. The method of  claim 7 , wherein said  Solanum lycopersicum  UBQ10 gene regulatory sequence comprises  Solanum lycopersicum  UBQ10 promoter and terminator regions. 
     
     
       9. The method of  claim 1 , wherein the homologous recombination between said donor sequence and said plant endogenous DNA sequence comprises gene editing, gene replacement, or a combination of both. 
     
     
       10. A recombinant nucleic acid molecule comprising a first nucleotide sequence encoding a nuclease system and a second nucleotide sequence encoding a viral replicon comprising a donor nucleic acid sequence targeted to a plant endogenous DNA sequence, wherein said nuclease system is targeted to said endogenous DNA sequence in said plant, and wherein at least one component of said nuclease system is operably linked to a UBQ10 gene regulatory sequence,
 wherein said UBQ10 gene regulatory sequence comprises:
 (a) a first regulatory region, wherein said first regulatory region comprises a first nucleic acid sequence from said UBQ10 gene where said first nucleic acid sequence extends about 2 Kb upstream of the coding region of said UBQ10 gene but not including the start codon, and wherein said first regulatory region is 5′ of said at least one component of said nuclease system; and 
 (b) a second regulatory region, wherein said second regulatory region comprises a second nucleic acid sequence from said UBQ10 gene where said second nucleic acid sequence extends about 1 Kb downstream of the coding region of said UBQ10 gene but not including the stop codon of said UBQ10 gene, and wherein said second regulatory region is 3′ of said at least one component of said nuclease system; 
 
 
       wherein said UBQ10 gene comprises the sequence set forth in nucleic acids 2076-3449 of SEQ ID NO: 22 or a homolog thereof having at least 90% identity with nucleic acids 2076-3449 of SEQ ID NO: 22, wherein said nuclease system is selected from a nickase, a CRISPR/Cas system, or a DNA endonuclease enzyme used in targeted gene editing, and 
       wherein said viral replicon is selected from the group consisting of: a geminiviral replicon, a BeYDV replicon, a CalCuV replicon, a ToLCV replicon, a WDV replicon, or any combination thereof. 
     
     
       11. The recombinant nucleic acid of  claim 10 , wherein said donor sequence comprises a gene, a mutated gene, a part of a gene, a regulatory sequence, a mutated regulatory sequence, a sequence upstream of a gene, a sequence downstream of a gene, an exon sequence, an intron sequence, or any combination thereof. 
     
     
       12. The recombinant nucleic acid of  claim 1 , wherein said CRISPR/Cas system comprises a Cas nuclease and a gRNA molecule, wherein said gRNA molecule binds within said plant endogenous DNA sequence. 
     
     
       13. The recombinant nucleic acid of  claim 12 , wherein said Cas nuclease is selected from the group consisting of Cas1, Cas1B, Cas2, Cas3, Cas4, Cass, Cas6, Cas7, Cas8, Cas9, Cas10, C2c1, CasX, NgAgo, Cpf1, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, and Csf4. 
     
     
       14. The recombinant nucleic acid of  claim 10 , wherein said at least one component of said nuclease system comprises a Cas nuclease. 
     
     
       15. The recombinant nucleic acid of  claim 14 , wherein said UBQ10 gene regulatory sequence comprises a  Solanum lycopersicum  or a  Solanum tuberosum  UBQ10 gene regulatory sequence. 
     
     
       16. The recombinant nucleic acid of  claim 15 , wherein said  Solanum lycopersicum  UBQ10 gene regulatory sequence comprises  Solamum lycopersicum  UBQ10 promoter and terminator regions. 
     
     
       17. A method for producing a transgenic plant seed, the method comprising:
 (a) introducing into at least one cell of a plant a first nucleic acid comprising a viral replicon comprising a donor nucleic acid sequence, said donor sequence targeted to an endogenous DNA sequence of said plant; and 
 (b) introducing into said at least one cell of a plant (a) a second nucleic acid comprising a nuclease system, wherein said nuclease system is targeted to said endogenous DNA sequence of said plant, and wherein at least one component of said nuclease system is expressed under the control of a UBQ10 gene regulatory sequence; 
 (c) generating a transgenic plant from said at least one cell of said plant; and 
 (d) growing said transgenic plant to obtain a seed; 
 wherein homologous recombination occurs between the donor sequence and said plant endogenous DNA sequence; 
 
       thereby producing a transgenic seed of the plant, wherein any plant produced from said seed comprises said donor nucleic acid sequence, 
       wherein said UBQ10 gene regulatory sequence comprises a recombinant nucleic acid molecule comprising:
 (a) a first regulatory region, wherein said first regulatory region comprises a fin nucleic acid sequence from said UBQ10 gene where said first nucleic acid sequence extends about 2 Kb upstream of the coding region of said UBQ10 gene but not including the start codon, and wherein said first regulatory region is 5′ of said at least one component of said nuclease system; and 
 (b) a second regulatory region, wherein said second regulatory region comprises a second nucleic acid sequence from said UBQ10 gene where said second nucleic acid sequence extends about 1 Kb downstream of the coding region of said UBQ10 gene but not including the stop codon, and wherein said second regulatory region is 3′ of said at least one component of said nuclease system; 
 
       wherein said UBQ10 gene comprises the sequence set forth in nucleic acids 2076-3449 of SEQ ID NO: 22 or a homolog thereof having at least 90% identity with nucleic acids 2076-3449 of SEQ ID NO: 22, wherein said nuclease system is selected from a nickase, a CRISPR/Cas system, or a DNA endonuclease enzyme used in targeted gene editing, and 
       wherein said viral replicon is selected from the group consisting of: a geminiviral replicon, a BeYDV replicon, a CalCuV replicon, a ToLCV replicon, a WDV replicon, or any combination thereof. 
     
     
       18. The method of  claim 17 , wherein said donor sequence comprises a gene, a mutated gene, a part of a gene, a regulatory sequence, a mutated regulatory sequence, a sequence upstream of a gene, a sequence downstream of a gene, an exon sequence, an intron sequence, or any combination thereof. 
     
     
       19. The method of  claim 17 , wherein said CRISPR/Cas system comprises a Cas nuclease and a gRNA molecule, wherein said gRNA molecule binds within said plant endogenous DNA sequence. 
     
     
       20. The method of  claim 19 , wherein said Cas nuclease is selected from the Group consisting of Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9, Cas10, C2c1, CasX, NgAgo, Cpf1, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, and Csf4. 
     
     
       21. The method of  claim 17 , wherein said at least one component of said nuclease system comprises a Cas nuclease. 
     
     
       22. The method of  claim 17 , wherein said first nucleic acid and said second nucleic acid are located on a single expression vector. 
     
     
       23. The method of  claim 17 , wherein said UBQ10 gene regulatory sequence comprises a  Solamum lycopersicum  or a  Solamum tuberosum  UBQ10 gene regulatory sequence. 
     
     
       24. The method of  claim 23 , wherein said  Solanum lycopersicum  UBQ10 gene regulatory sequence comprises  Solanum lycopersicum  UBQ10 promoter and terminator regions.